2IHJ

crystal structure of multifunctional sialyltransferase from pasteurella multocida with CMP-3F-Neu5Ac bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2EX1PDB ENTRY 2EX1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29325% PEG MME 2000 0.2 M NaBr 0.4% Triton X-100, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8757.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.805α = 90
b = 65.339β = 98.14
c = 66.795γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray109CCDMARMOSAIC 325 mm CCD2006-01-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.97944SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1266.0898.70.05115.33.23576535281
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0599.310.312.43.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2EX1266.083576533495176198.630.196490.195010.22336RANDOM31.676
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.681.10.07-0.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.08
r_dihedral_angle_4_deg14.133
r_dihedral_angle_3_deg13.743
r_dihedral_angle_1_deg5.219
r_scangle_it1.501
r_angle_refined_deg1.179
r_scbond_it0.961
r_mcangle_it0.652
r_mcbond_it0.417
r_nbtor_refined0.294
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.08
r_dihedral_angle_4_deg14.133
r_dihedral_angle_3_deg13.743
r_dihedral_angle_1_deg5.219
r_scangle_it1.501
r_angle_refined_deg1.179
r_scbond_it0.961
r_mcangle_it0.652
r_mcbond_it0.417
r_nbtor_refined0.294
r_nbd_refined0.173
r_symmetry_vdw_refined0.146
r_xyhbond_nbd_refined0.122
r_symmetry_hbond_refined0.114
r_chiral_restr0.076
r_bond_refined_d0.011
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3112
Nucleic Acid Atoms
Solvent Atoms422
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing